neurom.fst.get

neurom.fst.get(feature, obj, **kwargs)

Obtain a feature from a set of morphology objects

Parameters:

• feature (string) – feature to extract
• obj – a neuron, population or neurite tree
• **kwargs – parameters to forward to underlying worker functions

Returns:

features as a 1D or 2D numpy array.

Features:

Neurite features (neurite, neuron, neuron population):

• local_bifurcation_angles:

  Get a list of local bifurcation angles in a collection of neurites

• neurite_lengths:

  Get the path length per neurite in a collection

• neurite_volume_density:

  Get the volume density per neurite

  The volume density is defined as the ratio of the neurite volume and the volume of the neurite’s enclosing convex hull

• neurite_volumes:

  Get the volume per neurite in a collection

• number_of_bifurcations:

  number of bifurcation points in a collection of neurites

• number_of_forking_points:

  number of forking points in a collection of neurites

• number_of_neurites:

  Number of neurites in a collection of neurites

• number_of_sections:

  Number of sections in a collection of neurites

• number_of_sections_per_neurite:

  Get the number of sections per neurite in a collection of neurites

• number_of_segments:

  Number of sections in a collection of neurites

• number_of_terminations:

  number of leaves points in a collection of neurites

• partition:

  Partition at bifurcation points of a collection of neurites

• partition_asymmetry:

  Partition asymmetry at bifurcation points of a collection of neurites

• partition_pairs:

  Partition pairs at bifurcation points of a collection of neurites.

  Partition pait is defined as the number of bifurcations at the two daughters of the bifurcating section

• principal_direction_extents:

  Principal direction extent of neurites in neurons

• remote_bifurcation_angles:

  Get a list of remote bifurcation angles in a collection of neurites

• section_areas:

  section areas in a collection of neurites

• section_bif_branch_orders:

  Bifurcation section branch orders in a collection of neurites

• section_bif_lengths:

  Bifurcation section lengths in a collection of neurites

• section_bif_radial_distances:

  Get the radial distances of the bifurcation sections for a collection of neurites

• section_branch_orders:

  section branch orders in a collection of neurites

• section_end_distances:

  section end to end distances in a collection of neurites

• section_lengths:

  section lengths in a collection of neurites

• section_path_distances:

  Path lengths of a collection of neurites

• section_radial_distances:

  Section radial distances in a collection of neurites.

  The iterator_type can be used to select only terminal sections (ileaf) or only bifurcations (ibifurcation_point).

• section_strahler_orders:

  Inter-segment opening angles in a section

• section_term_branch_orders:

  Termination section branch orders in a collection of neurites

• section_term_lengths:

  Termination section lengths in a collection of neurites

• section_term_radial_distances:

  Get the radial distances of the termination sections for a collection of neurites

• section_tortuosity:

  section tortuosities in a collection of neurites

• section_volumes:

  section volumes in a collection of neurites

• segment_lengths:

  Lengths of the segments in a collection of neurites

• segment_meander_angles:

  Inter-segment opening angles in a section

• segment_midpoints:

  Return a list of segment mid-points in a collection of neurites

• segment_radial_distances:

  Lengths of the segments in a collection of neurites

• segment_radii:

  arithmetic mean of the radii of the points in segments in a collection of neurites

• segment_taper_rates:

  taper rates of the segments in a collection of neurites

  The taper rate is defined as the absolute radii differences divided by length of the section

• segment_volumes:

  Volumes of the segments in a collection of neurites

• terminal_path_lengths_per_neurite:

  Get the path lengths to each terminal point per neurite in a collection

• total_area_per_neurite:

  Surface area in a collection of neurites.

  The area is defined as the sum of the area of the sections.

• total_length:

  Get the total length of all sections in the group of neurons or neurites

• total_length_per_neurite:

  Get the path length per neurite in a collection

Neuron features (neuron, neuron population):

• sholl_frequency:

  perform Sholl frequency calculations on a population of neurites

  Args:

  nrn(morph): nrn or population neurite_type(NeuriteType): which neurites to operate on step_size(float): step size between Sholl radii

  Note:

  Given a neuron, the soma center is used for the concentric circles, which range from the soma radii, and the maximum radial distance in steps of step_size. When a population is given, the concentric circles range from the smallest soma radius to the largest radial neurite distance. Finally, each segment of the neuron is tested, so a neurite that bends back on itself, and crosses the same Sholl radius will get counted as having crossed multiple times.

• soma_radii:

  Get the radii of the somata of a population of neurons

  Note:

  If a single neuron is passed, a single element list with the radius of its soma member is returned.

• soma_surface_areas:

  Get the surface areas of the somata in a population of neurons

  Note:

  The surface area is calculated by assuming the soma is spherical.

  Note:

  If a single neuron is passed, a single element list with the surface area of its soma member is returned.

• trunk_angles:

  Calculates the angles between all the trunks of the neuron.

  The angles are defined on the x-y plane and the trees are sorted from the y axis and anticlock-wise.

• trunk_origin_azimuths:

  Get a list of all the trunk origin azimuths of a neuron or population

  The azimuth is defined as Angle between x-axis and the vector defined by (initial tree point - soma center) on the x-z plane.

  The range of the azimuth angle [-pi, pi] radians

• trunk_origin_elevations:

  Get a list of all the trunk origin elevations of a neuron or population

  The elevation is defined as the angle between x-axis and the vector defined by (initial tree point - soma center) on the x-y half-plane.

  The range of the elevation angle [-pi/2, pi/2] radians

• trunk_origin_radii:

  radii of the trunk sections of neurites in a neuron

• trunk_section_lengths:

  list of lengths of trunk sections of neurites in a neuron

• trunk_vectors:

  Calculates the vectors between all the trunks of the neuron

  and the soma center.